README.md

dockstore-tool-bamstats

A repo for the Dockerfile to create a Docker image for the BAMStats command. Also contains the Dockstore.yml which is used by the Dockstore to register this container and describe how to call BAMStats for the community.

Validation

This tool has been validated as a CWL draft-3 and v1.0 CommandLineTool.

Versions that we tested with are the following

avro (1.8.1)
cwl-runner (1.0)
cwl-upgrader (0.1.1)
cwltool (1.0.20160712154127)
schema-salad (1.14.20160708181155)
setuptools (25.1.6)

Building Manually

Normally you would let Quay.io build this. But, if you need to build manually you would execute:

docker build -t collaboratory/dockstore-tool-bamstats:1.25-3 .

Running Manually

$ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam collaboratory/dockstore-tool-bamstats:1.25-3

# within the docker container
$ /usr/local/bin/bamstats 4 /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam

You'll then see a file, bamstats_report.zip, in the current directory, that's the report file. You can use -v to mount the result out of the container.

Running Through the Dockstore CLI

This tool can be found at the Dockstore, login with your GitHub account and follow the directions to setup the CLI. It lets you run a Docker container with a CWL descriptor locally, using Docker and the CWL command line utility. This is great for testing.

Make a Parameters JSON

This is the parameterization of the BAM stat tool, a copy is present in this repo called sample_configs.json:

{
  "bam_input": {
        "class": "File",
        "path": "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"
    },
    "bamstats_report": {
        "class": "File",
        "path": "/tmp/bamstats_report.zip"
    }
}

Run with the CLI

Run it using the dockstore CLI:

Usage:
# fetch CWL
$> dockstore cwl --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 > Dockstore.cwl
# make a runtime JSON template and edit it (or use the content of sample_configs.json above)
$> dockstore convert cwl2json --cwl Dockstore.cwl > Dockstore.json
# run it locally with the Dockstore CLI
$> dockstore launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 \
    --json Dockstore.json